## [1] "O76_p2_IFNg_R1_2.hicup.bam"
Truncation & Mapping
Truncation Frequency
| Total |
50,062,192 |
50,062,192 |
| Not Truncated |
29,576,585 |
29,486,994 |
| Truncated |
20,485,607 |
20,575,198 |
Truncated Read Length
| Average Length Truncated |
46.2 |
47 |
Mapping Efficiency
| Too Short To Map |
3,466,681 |
3,177,920 |
| Unique Alignments |
42,923,607 |
41,770,569 |
| Multiple Alignments |
1,609,329 |
1,705,215 |
| Failed To Align |
2,062,575 |
3,408,488 |
| Paired |
36,230,756 |
36,230,756 |
Truncation and Mapping Bar Plot
Filtering
Filtering Breakdown by Category
| Valid Pairs |
19,116,826 |
| Invalid Pairs |
17,113,930 |
| Same Circularised |
78,105 |
| Same Dangling Ends |
2,381,099 |
| Same Fragment Internal |
8,651,550 |
| Re Ligation |
4,830,533 |
| Contiguous Sequence |
263,266 |
| Wrong Size |
909,377 |
| Total Pairs |
36,230,756 |
Filtering Breakdown Pie Chart
Ditag Length Distribution
Deduplication
Deduplication Summary Table
| Read Pairs |
19,116,826 |
27,918 |
| Cis-close (<10Kbp) |
1,824,464 |
2,667 |
| Cis-far (>10Kbp) |
11,797,025 |
14,940 |
| Trans |
5,495,337 |
10,311 |
Deduplication Bar Chart
Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data
